SS3D-P2: a three dimensional substructure search program for protein motifs based on secondary structure elements.
This paper discusses the implementation of a three-dimensional (3D) structure motif search of proteins. Each protein structure is represented by a set of secondary structure elements (SSEs) which involves alpha-helix segments and beta-strand segments. In describing it, every SSE is further reduced into a two-node graph that consists of the starting amino acid residue, the ending residue and a pseudo-bond between them. The searching algorithm is based on a graph theoretical clique-finding algorithm that has been used for 3D substructure searching in small organic molecules. The program SS3D-P2 was validated using proteins that have well-known 3D motifs, and it correctly found the Greek key motif within an eye lens protein, crystallin, that consists of four anti-parallel beta strands. The program was also successfully applied to searching for the more complex 3D motif, TIM-type beta-barrel motif, with a protein structure database from the Protein Data Bank.
Kato
H
H
Department of Knowledge-based Information Engineering, Toyohashi University of Technology, Japan. ¿hiro,taka¿@mis.tutkie.tut.ac.jp
Takahashi
Y
Y
D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D003459:Crystallins / Q000737:chemistry; D016208:Databases, Factual; D008958:Models, Molecular; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D017386:Sequence Homology, Amino Acid; D012984:Software
D003459:Crystallins; D011506:Proteins